Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-24 11:40 -0500 (Tue, 24 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 1398/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
netboost 2.15.0 (landing page) Pascal Schlosser
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | ... NOT SUPPORTED ... | ||||||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
To the developers/maintainers of the netboost package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/netboost.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: netboost |
Version: 2.15.0 |
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:netboost.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings netboost_2.15.0.tar.gz |
StartedAt: 2024-12-24 00:22:15 -0500 (Tue, 24 Dec 2024) |
EndedAt: 2024-12-24 00:25:23 -0500 (Tue, 24 Dec 2024) |
EllapsedTime: 187.2 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: netboost.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:netboost.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings netboost_2.15.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/netboost.Rcheck’ * using R Under development (unstable) (2024-10-21 r87258) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0 GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0 * running under: Ubuntu 24.04.1 LTS * using session charset: UTF-8 * checking for file ‘netboost/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘netboost’ version ‘2.15.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... NOTE Found the following hidden files and directories: .BBSoptions These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘netboost’ can be installed ... WARNING Found the following significant warnings: boosting.cpp:415:71: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] boosting.cpp:415:81: warning: format ‘%d’ expects argument of type ‘int’, but argument 5 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] boosting.cpp:645:44: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] HierarchicalClustering_with_unknown_edges.hpp:150:47: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations] HierarchicalClustering_with_unknown_edges.hpp:177:45: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations] HierarchicalClustering_with_unknown_edges.hpp:259:31: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations] See ‘/home/biocbuild/bbs-3.21-bioc/meat/netboost.Rcheck/00install.out’ for details. * used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ * checking C++ specification ... NOTE Specified C++11: please drop specification unless essential * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE BugReports field is not a suitable URL but appears to contain an email address not specified by mailto: nor contained in < > use the Contact field instead * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... OK * checking dependencies in R code ... NOTE Namespace in Imports field not imported from: ‘BiocStyle’ All declared Imports should be used. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... NOTE checkRd: (-1) cpp_filter_step.Rd:19: Lost braces 19 | Must be initialised before using @see{filter_base} | ^ * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking line endings in shell scripts ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... INFO GNU make is a SystemRequirements. * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking include directives in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed cut_trees 7.207 0.244 7.455 nb_summary 6.605 0.037 6.644 nb_mcupgma 6.492 0.142 6.634 tree_search 6.467 0.095 6.563 nb_clust 6.468 0.061 6.530 nb_dist 6.059 0.069 6.128 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 6 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/netboost.Rcheck/00check.log’ for details.
netboost.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL netboost ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘netboost’ ... ** using staged installation checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /usr/bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking whether gcc understands -c and -o together... yes checking whether make supports the include directive... yes (GNU style) checking dependency style of gcc... none checking how to run the C preprocessor... gcc -E checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking for x86 cpuid output... unknown checking for x86-AVX xgetbv output... unknown checking for x86 cpuid 0x00000000 output... 16:756e6547:6c65746e:49656e69 checking for x86 cpuid 0x80000000 output... 80000008:0:0:0 checking for x86 cpuid 0x00000001 output... 50657:20400800:7ffefbff:bfebfbff checking for x86 cpuid 0x00000007 output... 0:d39ff7eb:818:bc000400 checking for x86 cpuid 0x80000001 output... 0:0:121:2c100800 checking for x86-AVX xgetbv 0x00000000 output... 2ff:0 checking whether RDRND is supported by the processor... yes checking whether RDRND is supported by the processor and OS... yes checking whether C compiler accepts -mrdrnd... yes checking whether BMI1 is supported by the processor... yes checking whether BMI1 is supported by the processor and OS... yes checking whether C compiler accepts -mbmi... yes checking whether BMI2 is supported by the processor... yes checking whether BMI2 is supported by the processor and OS... yes checking whether C compiler accepts -mbmi2... yes checking whether ADX is supported by the processor... yes checking whether ADX is supported by the processor and OS... yes checking whether C compiler accepts -madx... yes checking whether MPX is supported by the processor... yes checking whether MPX is supported by the processor and OS... yes checking whether C compiler accepts -mmpx... yes checking whether PREFETCHWT1 is supported by the processor... no checking whether ABM is supported by the processor... yes checking whether ABM is supported by the processor and OS... yes checking whether C compiler accepts -mabm... yes checking whether MMX is supported by the processor... yes checking whether MMX is supported by the processor and OS... yes checking whether C compiler accepts -mmmx... yes checking whether SSE is supported by the processor... yes checking whether SSE is supported by the processor and OS... yes checking whether C compiler accepts -msse... yes checking whether SSE2 is supported by the processor... yes checking whether SSE2 is supported by the processor and OS... yes checking whether C compiler accepts -msse2... yes checking whether SSE3 is supported by the processor... yes checking whether SSE3 is supported by the processor and OS... yes checking whether C compiler accepts -msse3... yes checking whether SSSE3 is supported by the processor... yes checking whether SSSE3 is supported by the processor and OS... yes checking whether C compiler accepts -mssse3... yes checking whether SSE4.1 is supported by the processor... yes checking whether SSE4.1 is supported by the processor and OS... yes checking whether C compiler accepts -msse4.1... yes checking whether SSE4.2 is supported by the processor... yes checking whether SSE4.2 is supported by the processor and OS... yes checking whether C compiler accepts -msse4.2... yes checking whether SSE4a is supported by the processor... no checking whether SHA is supported by the processor... no checking whether AES is supported by the processor... yes checking whether AES is supported by the processor and OS... yes checking whether C compiler accepts -maes... yes checking whether AVX is supported by the processor... yes checking whether AVX is supported by the processor and OS... yes checking whether C compiler accepts -mavx... yes checking whether FMA3 is supported by the processor... yes checking whether FMA3 is supported by the processor and OS... yes checking whether C compiler accepts -mfma... yes checking whether FMA4 is supported by the processor... no checking whether XOP is supported by the processor... no checking whether AVX2 is supported by the processor... yes checking whether AVX2 is supported by the processor and OS... yes checking whether C compiler accepts -mavx2... yes checking whether AVX512-F is supported by the processor... yes checking whether AVX512-F is supported by the processor and OS... yes checking whether C compiler accepts -mavx512f... yes checking whether AVX512-CD is supported by the processor... yes checking whether AVX512-CD is supported by the processor and OS... yes checking whether C compiler accepts -mavx512cd... yes checking whether AVX512-PF is supported by the processor... no checking whether AVX512-ER is supported by the processor... no checking whether AVX512-VL is supported by the processor... yes checking whether AVX512-VL is supported by the processor and OS... yes checking whether C compiler accepts -mavx512vl... yes checking whether AVX512-BW is supported by the processor... yes checking whether AVX512-BW is supported by the processor and OS... yes checking whether C compiler accepts -mavx512bw... yes checking whether AVX512-DQ is supported by the processor... yes checking whether AVX512-DQ is supported by the processor and OS... yes checking whether C compiler accepts -mavx512dq... yes checking whether AVX512-IFMA is supported by the processor... no checking whether AVX512-VBMI is supported by the processor... no checking whether C compiler accepts -Wno-deprecated... yes checking for strip... strip checking that generated files are newer than configure... done configure: creating ./config.status config.status: creating src/Makevars config.status: creating src/mcupgma/clustering_util/Makefile config.status: creating src/config.h config.status: executing depfiles commands ** libs using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ using C++11 g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppParallel/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 `/home/biocbuild/bbs-3.21-bioc/R/bin/Rscript -e "Rcpp:::CxxFlags()"` -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -maes -mavx -mfma -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -mavx512dq -fpic -g -O2 -Wall -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppParallel/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 `/home/biocbuild/bbs-3.21-bioc/R/bin/Rscript -e "Rcpp:::CxxFlags()"` -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -maes -mavx -mfma -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -mavx512dq -fpic -g -O2 -Wall -DR_NO_REMAP -c boosting.cpp -o boosting.o boosting.cpp: In constructor ‘Boosting::Boosting(const Rcpp::NumericMatrix&, unsigned int, double)’: boosting.cpp:415:71: warning: format ‘%d’ expects argument of type ‘int’, but argument 4 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 415 | Rprintf( " DATA POINTER REAL LENGTH: %li / %li dbl (matrix: %d -- max %d)\n", | ~^ | | | int | %ld ...... 418 | (col+1) * nrow, | ~~~~~~~~~~~~~~ | | | size_t {aka long unsigned int} boosting.cpp:415:81: warning: format ‘%d’ expects argument of type ‘int’, but argument 5 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 415 | Rprintf( " DATA POINTER REAL LENGTH: %li / %li dbl (matrix: %d -- max %d)\n", | ~^ | | | int | %ld ...... 419 | (col+1) * (nrow + 256/sizeof(double)) | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | | | size_t {aka long unsigned int} boosting.cpp: In instantiation of ‘Rcpp::IntegerVector Boosting::filter_column_gen(size_t) [with bool AVX = true; bool FMA = false; bool ALIGNED = true; Rcpp::IntegerVector = Rcpp::Vector<13>; size_t = long unsigned int]’: boosting.cpp:729:53: required from here boosting.cpp:645:44: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 645 | Rprintf( "C STEP: %d (ACTUAL_SEL: %d, UPDATE: %f)\n ", | ~^ | | | int | %ld 646 | bstep + 1, actual_sel + 1, actual_update); | ~~~~~~~~~~~~~~ | | | size_t {aka long unsigned int} boosting.cpp: In instantiation of ‘Rcpp::IntegerVector Boosting::filter_column_gen(size_t) [with bool AVX = false; bool FMA = false; bool ALIGNED = true; Rcpp::IntegerVector = Rcpp::Vector<13>; size_t = long unsigned int]’: boosting.cpp:732:54: required from here boosting.cpp:645:44: warning: format ‘%d’ expects argument of type ‘int’, but argument 3 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=] 645 | Rprintf( "C STEP: %d (ACTUAL_SEL: %d, UPDATE: %f)\n ", | ~^ | | | int | %ld 646 | bstep + 1, actual_sel + 1, actual_update); | ~~~~~~~~~~~~~~ | | | size_t {aka long unsigned int} g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppParallel/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 `/home/biocbuild/bbs-3.21-bioc/R/bin/Rscript -e "Rcpp:::CxxFlags()"` -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -maes -mavx -mfma -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -mavx512dq -fpic -g -O2 -Wall -DR_NO_REMAP -c dist_tom.cpp -o dist_tom.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/RcppParallel/include' -I/usr/local/include -DSTRICT_R_HEADERS=1 `/home/biocbuild/bbs-3.21-bioc/R/bin/Rscript -e "Rcpp:::CxxFlags()"` -mmmx -msse -msse2 -msse3 -mssse3 -msse4.1 -msse4.2 -maes -mavx -mfma -mavx2 -mavx512f -mavx512cd -mavx512vl -mavx512bw -mavx512dq -fpic -g -O2 -Wall -DR_NO_REMAP -c tree_sort.cpp -o tree_sort.o g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.21-bioc/R/lib -L/usr/local/lib -o netboost.so RcppExports.o boosting.o dist_tom.o tree_sort.o -L/home/biocbuild/bbs-3.21-bioc/R/lib -lR strip -S netboost.so installing via 'install.libs.R' to /home/biocbuild/bbs-3.21-bioc/R/site-library/00LOCK-netboost/00new/netboost [1] "R_PACKAGE_SRC: /home/biocbuild/bbs-3.21-bioc/meat/netboost" [1] "R_PACKAGE_DIR: /home/biocbuild/bbs-3.21-bioc/R/site-library/00LOCK-netboost/00new/netboost" [1] "R_ARCH: " [1] "SHLIB_EXT: .so" [1] "INSTALL PATH: /home/biocbuild/bbs-3.21-bioc/meat/netboost/src/mcupgma/scripts/install_path.mk" make: Entering directory '/home/biocbuild/bbs-3.21-bioc/meat/netboost/src/mcupgma' Clean build. make: Leaving directory '/home/biocbuild/bbs-3.21-bioc/meat/netboost/src/mcupgma' make: Entering directory '/home/biocbuild/bbs-3.21-bioc/meat/netboost/src/mcupgma' ==== compiling clustering_util sources using external Makefile (clustering_util/Makefile) recursively make -C clustering_util -f Makefile mcupgma_install make[1]: Entering directory '/home/biocbuild/bbs-3.21-bioc/meat/netboost/src/mcupgma/clustering_util' mkdir -p bin mkdir -p obj.x86_64_Linux g++ -Wall -Wno-deprecated -O3 -DNDEBUG -c -o obj.x86_64_Linux/HashingMergerMain.cmdline.o HashingMergerMain.cmdline.c g++ -Wall -Wno-deprecated -O3 -DNDEBUG -Wall -Wno-deprecated -O3 -DNDEBUG -c -o obj.x86_64_Linux/ClusteringUtil.o ClusteringUtil.cpp g++ -Wall -Wno-deprecated -O3 -DNDEBUG -Wall -Wno-deprecated -O3 -DNDEBUG -c -o obj.x86_64_Linux/Tree.o Tree.cpp g++ -Wall -Wno-deprecated -O3 -DNDEBUG -o bin/edges2valid_clusters HashingMergerMain.cpp obj.x86_64_Linux/HashingMergerMain.cmdline.o obj.x86_64_Linux/ClusteringUtil.o obj.x86_64_Linux/Tree.o g++ -Wall -Wno-deprecated -O3 -DNDEBUG -c -o obj.x86_64_Linux/EdgeCollatorMain.cmdline.o EdgeCollatorMain.cmdline.c g++ -Wall -Wno-deprecated -O3 -DNDEBUG -o bin/edge_collator EdgeCollatorMain.cpp obj.x86_64_Linux/EdgeCollatorMain.cmdline.o obj.x86_64_Linux/ClusteringUtil.o obj.x86_64_Linux/Tree.o make[1]: Leaving directory '/home/biocbuild/bbs-3.21-bioc/meat/netboost/src/mcupgma/clustering_util' ==== compiling sources using external Makefile (clustering_round/Makefile) recursively make -C clustering_round -f Makefile make[1]: Entering directory '/home/biocbuild/bbs-3.21-bioc/meat/netboost/src/mcupgma/clustering_round' mkdir -p dep.x86_64_Linux test -d dep.x86_64_Linux && g++ -MM -MT 'dep.x86_64_Linux/test_heap.d obj.x86_64_Linux/test_heap.o obj.x86_64_Linux.debug/test_heap.o' -O3 -ftemplate-depth-64 -I./ test_heap.cpp > dep.x86_64_Linux/test_heap.d test -d dep.x86_64_Linux && g++ -MM -MT 'dep.x86_64_Linux/HierarchicalClustering_with_unknown_edges.d obj.x86_64_Linux/HierarchicalClustering_with_unknown_edges.o obj.x86_64_Linux.debug/HierarchicalClustering_with_unknown_edges.o' -O3 -ftemplate-depth-64 -I./ HierarchicalClustering_with_unknown_edges.cpp > dep.x86_64_Linux/HierarchicalClustering_with_unknown_edges.d test -d dep.x86_64_Linux && g++ -MM -MT 'dep.x86_64_Linux/HierarchicalClustering_main.d obj.x86_64_Linux/HierarchicalClustering_main.o obj.x86_64_Linux.debug/HierarchicalClustering_main.o' -O3 -ftemplate-depth-64 -I./ HierarchicalClustering_main.cpp > dep.x86_64_Linux/HierarchicalClustering_main.d test -d dep.x86_64_Linux && g++ -MM -MT 'dep.x86_64_Linux/test_heap.d obj.x86_64_Linux/test_heap.o obj.x86_64_Linux.debug/test_heap.o' -O3 -ftemplate-depth-64 -I./ test_heap.cpp > dep.x86_64_Linux/test_heap.d test -d dep.x86_64_Linux && g++ -MM -MT 'dep.x86_64_Linux/HierarchicalClustering_with_unknown_edges.d obj.x86_64_Linux/HierarchicalClustering_with_unknown_edges.o obj.x86_64_Linux.debug/HierarchicalClustering_with_unknown_edges.o' -O3 -ftemplate-depth-64 -I./ HierarchicalClustering_with_unknown_edges.cpp > dep.x86_64_Linux/HierarchicalClustering_with_unknown_edges.d mkdir -p obj.x86_64_Linux mkdir -p bin g++ -O3 -ftemplate-depth-64 -I./ -c HierarchicalClustering_main.cpp -o obj.x86_64_Linux/HierarchicalClustering_main.o In file included from HierarchicalClustering_main.cpp:96: HierarchicalClustering_with_unknown_edges.hpp:150:47: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 150 | struct fCompareEdgesByLowerBound : public binary_function<tEdge, tEdge, bool> { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from HierarchicalClustering_with_unknown_edges.hpp:40: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ HierarchicalClustering_with_unknown_edges.hpp:177:45: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 177 | struct fCompareEdgesByUpperBound : public binary_function<tEdge, tEdge, bool> { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ HierarchicalClustering_with_unknown_edges.hpp:259:31: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 259 | struct fIsClusterInvalid : unary_function<tClusterId, bool> { | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ cc -O3 -I./ -c HierarchicalClustering_main.cmdline.c -o obj.x86_64_Linux/HierarchicalClustering_main.cmdline.o g++ -O3 -ftemplate-depth-64 -I./ -c HierarchicalClustering_with_unknown_edges.cpp -o obj.x86_64_Linux/HierarchicalClustering_with_unknown_edges.o In file included from HierarchicalClustering_with_unknown_edges.cpp:28: HierarchicalClustering_with_unknown_edges.hpp:150:47: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 150 | struct fCompareEdgesByLowerBound : public binary_function<tEdge, tEdge, bool> { | ^~~~~~~~~~~~~~~ In file included from /usr/include/c++/13/bits/refwrap.h:39, from /usr/include/c++/13/vector:68, from HierarchicalClustering_with_unknown_edges.hpp:40: /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ HierarchicalClustering_with_unknown_edges.hpp:177:45: warning: ‘template<class _Arg1, class _Arg2, class _Result> struct std::binary_function’ is deprecated [-Wdeprecated-declarations] 177 | struct fCompareEdgesByUpperBound : public binary_function<tEdge, tEdge, bool> { | ^~~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:131:12: note: declared here 131 | struct binary_function | ^~~~~~~~~~~~~~~ HierarchicalClustering_with_unknown_edges.hpp:259:31: warning: ‘template<class _Arg, class _Result> struct std::unary_function’ is deprecated [-Wdeprecated-declarations] 259 | struct fIsClusterInvalid : unary_function<tClusterId, bool> { | ^~~~~~~~~~~~~~ /usr/include/c++/13/bits/stl_function.h:117:12: note: declared here 117 | struct unary_function | ^~~~~~~~~~~~~~ g++ obj.x86_64_Linux/HierarchicalClustering_main.o obj.x86_64_Linux/HierarchicalClustering_main.cmdline.o obj.x86_64_Linux/HierarchicalClustering_with_unknown_edges.o -o bin/hierarchical_clustering -O3 g++ -O3 -ftemplate-depth-64 -I./ -c test_heap.cpp -o obj.x86_64_Linux/test_heap.o cc -O3 -I./ -c test_heap.cmdline.c -o obj.x86_64_Linux/test_heap.cmdline.o g++ obj.x86_64_Linux/test_heap.o obj.x86_64_Linux/test_heap.cmdline.o -o bin/test_heap -O3 make[1]: Leaving directory '/home/biocbuild/bbs-3.21-bioc/meat/netboost/src/mcupgma/clustering_round' make: Leaving directory '/home/biocbuild/bbs-3.21-bioc/meat/netboost/src/mcupgma' [1] "SRC: /home/biocbuild/bbs-3.21-bioc/meat/netboost/src/mcupgma" [1] "DEST: /home/biocbuild/bbs-3.21-bioc/R/site-library/00LOCK-netboost/00new/netboost/mcupgma" [1] "INSTALL FROM: /home/biocbuild/bbs-3.21-bioc/meat/netboost/src/mcupgma/clustering_round/bin TO: /home/biocbuild/bbs-3.21-bioc/R/site-library/00LOCK-netboost/00new/netboost/mcupgma" [1] "INSTALL FROM: /home/biocbuild/bbs-3.21-bioc/meat/netboost/src/mcupgma/clustering_util/bin TO: /home/biocbuild/bbs-3.21-bioc/R/site-library/00LOCK-netboost/00new/netboost/mcupgma" [1] "INSTALL FROM: /home/biocbuild/bbs-3.21-bioc/meat/netboost/src/mcupgma/scripts TO: /home/biocbuild/bbs-3.21-bioc/R/site-library/00LOCK-netboost/00new/netboost/mcupgma" [1] "netboost.so" ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (netboost)
netboost.Rcheck/netboost-Ex.timings
name | user | system | elapsed | |
cut_trees | 7.207 | 0.244 | 7.455 | |
dot-onAttach | 0 | 0 | 0 | |
mcupgma_exec | 0.017 | 0.008 | 0.024 | |
nb_clust | 6.468 | 0.061 | 6.530 | |
nb_dist | 6.059 | 0.069 | 6.128 | |
nb_filter | 4.094 | 0.025 | 4.119 | |
nb_mcupgma | 6.492 | 0.142 | 6.634 | |
nb_plot_dendro | 0.988 | 0.012 | 1.000 | |
nb_summary | 6.605 | 0.037 | 6.644 | |
nb_transfer | 0.969 | 0.001 | 0.969 | |
netboost | 1.006 | 0.002 | 1.008 | |
tree_search | 6.467 | 0.095 | 6.563 | |